AMBER Archive (2009)

Subject: Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old)

From: FyD (
Date: Tue Jul 28 2009 - 06:59:51 CDT

Dear Ashish Runthala,

> you can do with these grep commands, but it will do for all, and not
> all protons are insignificant. Remember here, that such protons seems
> weak bonds, but even then they are responsible for the stability of
> the overall confirmation. Check the structure in leap and protonate in
> a standard fashion, there, after removing the errors and warnings in
> leap.
> My advise is to properly verify the structure before stepping further.
> What you are working it out for by the way?

As said Bill egrep is perfect for that.
You could egrep using specific hydrogen names.

egrep -v "HB2|HB3" my.pdb > my_no-HB2HB3.pdb
egrep -v "HA2|HA3|HB1|HB2|HB3" my.pdb > my_no-selected-H.pdb

regards, Francois

> On Mon, Jul 27, 2009 at 9:17 AM, Bill Ross<> wrote:
>>>  how can I proceed to remove proton in protein
>> % egrep -v H my.pdb > my_no_h.pdb
>> Bill

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